BIOMretrieval: Get annotation information of samples as BIOM data

In matR: Metagenomics Analysis Tools

Description

Retrieve annotation pipeline information (such as abundance profiles) for specified metagenomes and projects into an object of class biom.

Usage

biomRequest(x, request=c("function", "organism"), ...,
  block, wait=TRUE, quiet=FALSE, file, outfile)

## S3 method for class 'environment'
biom(x, wait=TRUE, ..., quiet=FALSE)

Arguments

x	a set of metagenomes and/or projects (character) or a request ticket (environment)
request	choice of annotation type (string)
...	arguments specifying or qualifying the data desired (biomRequest() only)
block	number of metagenomes per API call (integer)
wait	return only when data is complete? (logical)
quiet	suppress messages and warnings? (logical)
file	file containing a set of metagenomes or projects (string)
outfile	file to save the retrieved data (string)

Details

Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.

Value

For biomRequest(), an environment if wait=FALSE. Otherwise and for biom.environment(), a biom object.

Author(s)

Daniel T. Braithwaite

See Also

BIOM.utils::biom, MGRASTer::call.MGRAST

Examples

####  several files demonstrate valid formats for ID input
demoSets()

## Not run: 
ff <- demoSets()

####  simple retrieval of annotation data
yy <- biomRequest (file=ff[1])
head (rows (yy))

####  many arguments can modify what is retrieved
yy <- biomRequest (file=ff[1], group_level="level1")
rownames (yy)

####  taxonomic annotations
yy <- biomRequest (file=ff[4], request="organism", group_level="phylum", source="Greengenes")

####  IDs can be given directly, while output can be to a file
biomRequest ("mgp9", request="function", outfile=file.path(tempdir("mgp9.biom")))
biomRequest ("mgm4441619.3 mgm4441620.3 mgm4441656.4", 
  request="function", outfile=file.path(tempdir("mgp9.biom")))

####  place an asynchronous request...
yy <- biomRequest ("mgp9", wait=FALSE)
####  ...and receive the data when convenient
yy <- biom (yy)

## End(Not run)

####  full detail for available options
doc.MGRAST (3, head=c("matrix","function","parameters","options"))
doc.MGRAST (3, head=c("matrix","organism","parameters","options"))

matR documentation built on May 2, 2019, 6:53 a.m.